Phylogenetics

Overview

Phylogenetic analysis reconstructs the evolutionary history of biological sequences (genes, proteins, genomes) by inferring the branching pattern of descent. This skill covers the standard pipeline:

1. MAFFT, Multiple sequence alignment
2. IQ-TREE 2, Maximum likelihood tree inference with model selection
3. FastTree, Fast approximate maximum likelihood (for large datasets)
4. ETE3, Python library for tree manipulation and visualization

Installation:

# Conda (recommended for CLI tools)
conda install -c bioconda mafft iqtree fasttree
pip install ete3

When to Use This Skill

Use phylogenetics when:

• Evolutionary relationships: Which organism/gene is most closely related to my sequence?
• Viral phylodynamics: Trace outbreak spread and estimate transmission dates
• Protein family analysis: Infer evolutionary relationships within a gene family
• Horizontal gene transfer detection: Identify genes with discordant species/gene trees
• Ancestral sequence reconstruction: Infer ancestral protein sequences
• Molecular clock analysis: Estimate divergence dates using temporal sampling
• GWAS companion: Place variants in evolutionary context (e.g., SARS-CoV-2 variants)
• Microbiology: Species phylogeny from 16S rRNA or core genome phylogeny

Standard Workflow

1. Multiple Sequence Alignment with MAFFT

import subprocess
import os

def run_mafft(input_fasta: str, output_fasta: str, method: str = "auto",
               n_threads: int = 4) -> str:
    """
    Align sequences with MAFFT.

    Args:
        input_fasta: Path to unaligned FASTA file
        output_fasta: Path for aligned output
        method: 'auto' (auto-select), 'einsi' (accurate), 'linsi' (accurate, slow),
                'fftnsi' (medium), 'fftns' (fast), 'retree2' (fast)
        n_threads: Number of CPU threads